Contacts of the strand formed by residues 172 - 180 (chain K) in PDB entry 5IJO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 172 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167K LEU 3.9 0.7 - - - +
168K ALA* 3.5 1.7 - - - +
169K THR* 2.8 36.0 + - - +
170K PRO 3.7 0.2 - - - -
171K VAL* 1.4 83.6 - - + +
173K ILE* 1.4 64.0 + - - +
174K VAL* 6.0 1.1 - - + -
207K SER* 4.5 14.6 - - - -
208K LEU 3.2 10.3 - - - +
209K PRO* 5.1 1.1 - - + -
210K THR* 5.1 3.4 - - - -
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Residues in contact with ILE 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K VAL* 6.4 1.3 - - + -
167K LEU 3.2 8.3 - - - +
168K ALA* 4.3 8.7 - - + +
172K ASP* 1.4 75.1 - - - +
174K VAL* 1.3 60.6 + - - +
205K LEU 3.6 7.4 - - - +
207K SER* 3.7 2.3 - - - -
208K LEU* 3.0 41.7 + - + +
210K THR* 5.4 5.8 - - - -
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Residues in contact with VAL 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K LEU 3.6 1.0 - - - +
166K VAL* 3.5 3.8 - - - -
167K LEU* 2.8 41.0 + - + +
172K ASP* 4.1 2.0 - - + -
173K ILE* 1.3 75.9 - - - +
175K ILE* 1.3 61.7 + - - +
176K LEU* 4.2 0.7 - - + -
205K LEU 3.6 9.2 - - - +
207K SER* 5.4 1.1 - - - +
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Residues in contact with ILE 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K LEU* 5.6 5.8 - - + -
165K LEU 3.5 4.9 - - - +
166K VAL* 4.7 3.6 - - + +
174K VAL* 1.3 76.9 - - - +
176K LEU* 1.3 61.6 - - - +
202K PRO* 4.5 0.7 - - - +
203K ASP* 3.2 30.9 + - + +
205K LEU* 3.8 23.9 + - + -
240K TYR* 6.3 2.5 - - + -
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Residues in contact with LEU 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K LEU* 3.3 8.8 - - - +
165K LEU* 2.8 41.3 + - + +
174K VAL* 6.3 0.4 - - + -
175K ILE* 1.3 75.6 - - - +
177K GLY* 1.3 64.1 + - - +
200K LEU* 5.3 5.6 - - + -
201K LEU 3.3 19.7 - - - +
202K PRO* 4.3 4.3 - - + -
203K ASP* 4.2 3.6 - - - +
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Residues in contact with GLY 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K VAL* 5.2 7.4 - - - -
163K HIS 3.9 6.3 - - - -
164K LEU* 4.6 1.1 - - - -
165K LEU* 5.2 1.3 - - - -
176K LEU* 1.3 76.0 - - - +
178K LEU* 1.3 59.4 + - - -
199K GLN 3.3 0.9 - - - +
200K LEU* 3.2 10.6 - - - +
201K LEU* 2.9 33.9 + - - +
203K ASP* 5.0 2.9 - - - +
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Residues in contact with LEU 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K ILE* 6.6 0.4 - - + -
161K VAL* 4.3 3.6 - - - +
162K ARG* 4.3 6.8 + - - +
163K HIS* 3.2 39.7 + - + +
164K LEU* 4.8 3.8 - - - +
165K LEU* 5.6 5.6 - - + +
176K LEU 4.2 0.4 + - - -
177K GLY* 1.3 74.1 - - - -
179K SER* 1.3 64.5 + - - +
199K GLN 3.4 4.5 - - - -
200K LEU* 4.9 1.3 - - - +
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Residues in contact with SER 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K VAL* 5.6 6.1 - - - -
162K ARG* 5.6 6.3 - - - -
178K LEU* 1.3 77.8 - - - +
180K TYR* 1.3 64.2 - - - +
198K MET* 3.6 5.0 - - - +
199K GLN* 2.8 39.8 + - - -
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Residues in contact with TYR 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K SER* 1.3 79.6 - - - +
181K ALA* 1.3 70.3 + - - +
182K ASN* 3.3 3.9 + - - -
196K GLY* 5.1 3.4 - - - +
197K GLY 3.4 8.5 - - - +
198K MET* 4.8 0.2 - - - +
199K GLN* 5.5 1.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il